Contacts of the helix formed by residues 114 - 132 (chain A) in PDB entry 2PPQ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLU 114 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A LYS 3.9 10.0 - - - +
113A PRO* 1.3 79.8 - - - +
115A ALA* 1.3 68.8 + - - +
116A LYS* 3.1 31.2 + - + +
117A HIS* 2.9 32.2 + - + +
118A CYS* 3.3 9.9 + - - -
243A LYS* 4.3 6.7 - - - +
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Residues in contact with ALA 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A GLU* 1.3 73.6 - - - +
116A LYS* 1.3 62.0 + - - +
118A CYS* 3.0 13.5 + - - +
119A ARG 3.2 0.2 + - - -
240A ASN* 5.9 0.2 - - - +
242A THR* 3.6 48.2 - - + +
243A LYS* 3.8 18.5 - - + +
246A ALA* 3.1 22.6 - - + +
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Residues in contact with LYS 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A GLU* 3.1 24.7 + - + +
115A ALA* 1.3 77.2 - - - +
117A HIS* 1.3 73.4 + - + +
119A ARG* 3.5 18.3 + - - +
120A GLU* 3.5 17.4 + - - +
204A ASP* 3.5 33.9 + - + +
246A ALA* 5.2 0.2 - - - -
323A MG 3.4 19.0 - - - -
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Residues in contact with HIS 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A LEU* 3.5 30.7 - - + +
112A LYS 4.7 1.4 + - - -
113A PRO* 3.8 8.1 - - + -
114A GLU* 2.9 53.8 + - + +
116A LYS* 1.3 81.5 - - + +
118A CYS* 1.3 64.7 + - - +
120A GLU* 3.1 7.7 + - - +
121A VAL* 3.0 25.1 + - - +
201A PHE* 3.7 25.1 - - + -
203A GLY 4.4 2.0 - - - -
204A ASP* 2.9 42.8 + - + +
231A TRP* 5.1 1.1 - - + -
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Residues in contact with CYS 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A PRO* 5.1 1.8 - - - -
114A GLU 3.8 7.4 - - - -
115A ALA 3.0 9.3 + - - +
117A HIS* 1.3 80.0 - - - +
119A ARG* 1.3 56.0 + - - +
121A VAL* 3.3 11.6 + - - +
122A GLY 3.0 22.9 + - - -
231A TRP* 3.9 34.5 - - - -
232A CYS* 4.9 0.4 - - - -
243A LYS* 3.8 50.5 - - - +
247A LEU* 3.5 16.8 - - + +
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Residues in contact with ARG 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A ALA 3.2 5.8 + - - +
116A LYS* 3.5 14.8 - - - +
117A HIS 3.2 0.6 - - - -
118A CYS* 1.3 73.0 - - - +
120A GLU* 1.3 68.2 + - - +
122A GLY 3.3 1.2 + - - -
123A LYS* 3.0 44.6 + - - +
245A LYS* 4.4 7.3 - - - +
246A ALA* 3.3 38.3 - - + +
249A GLU* 2.9 45.5 + - - +
250A GLY* 3.7 12.4 - - - +
253A SER* 5.9 1.8 - - - -
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Residues in contact with GLU 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A LYS 3.5 12.3 + - - +
117A HIS 3.1 7.5 + - - +
119A ARG* 1.3 81.1 - - - +
121A VAL* 1.3 56.6 + - - +
123A LYS* 3.1 37.7 + - - +
124A ALA* 2.9 30.3 + - - +
201A PHE* 3.9 14.6 - - + -
204A ASP 3.9 20.2 - - - +
205A GLU* 4.5 11.7 - - - +
206A LEU* 3.7 18.1 + - + +
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Residues in contact with VAL 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A HIS 3.0 19.4 + - - +
118A CYS* 3.4 9.6 - - - +
119A ARG 3.2 0.2 - - - -
120A GLU* 1.3 75.1 - - - +
122A GLY* 1.3 57.1 + - - +
124A ALA* 3.4 1.6 + - - +
125A LEU* 2.9 28.4 + - - +
194A LEU* 4.1 19.3 - - + +
199A VAL* 4.3 2.7 - - + -
201A PHE* 4.2 9.9 - - + -
206A LEU* 3.9 11.2 - - + -
227A CYS* 4.5 4.5 - - - -
231A TRP* 3.6 55.6 - - + +
247A LEU* 4.0 13.0 - - + -
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Residues in contact with GLY 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A CYS 3.0 10.9 + - - -
119A ARG 3.3 1.7 + - - -
121A VAL* 1.3 77.0 - - - +
123A LYS* 1.3 60.6 + - - +
125A LEU* 3.5 4.0 + - - -
126A ALA 3.1 18.7 + - - -
247A LEU* 3.5 32.4 - - - +
251A TYR* 3.2 23.6 - - - -
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Residues in contact with LYS 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A ARG* 3.0 33.3 + - - +
120A GLU* 3.1 40.1 + - - +
122A GLY* 1.3 76.5 - - - +
124A ALA* 1.3 57.5 + - - +
126A ALA* 3.5 2.8 + - - +
127A ALA* 3.0 28.0 + - - +
250A GLY* 3.3 21.2 - - - +
253A SER* 3.5 16.6 - - - +
254A VAL* 3.9 16.0 - - + +
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Residues in contact with ALA 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A LEU* 4.4 2.5 - - + +
120A GLU 2.9 16.4 + - - +
121A VAL 3.7 3.1 - - - +
123A LYS* 1.3 73.7 - - - +
125A LEU* 1.3 60.0 + - - +
127A ALA* 3.3 7.5 + - - +
128A MSE 2.9 29.5 + - - +
206A LEU* 3.6 30.7 - - + -
209A LEU* 4.0 18.4 - - + +
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Residues in contact with LEU 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A VAL 2.9 20.3 + - - +
122A GLY* 3.9 5.2 - - - +
124A ALA* 1.3 68.3 - - - +
126A ALA* 1.3 60.1 + - - +
128A MSE 3.3 22.5 + - + +
129A HIS* 2.9 50.4 + - + +
191A HIS* 4.7 0.2 - - + -
194A LEU* 4.0 25.3 - - + +
209A LEU* 4.9 0.4 - - - +
223A ASP* 3.2 25.1 - - - +
224A VAL* 3.9 29.2 - - + +
227A CYS* 3.9 18.4 - - + -
247A LEU* 6.0 1.1 - - + -
251A TYR* 4.0 10.8 - - + -
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Residues in contact with ALA 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A GLY 3.1 11.4 + - - +
123A LYS 3.7 4.0 - - - +
125A LEU* 1.3 74.9 - - - +
127A ALA* 1.3 65.0 + - - +
129A HIS* 3.1 3.9 + - - +
130A LEU* 2.9 26.7 + - - +
251A TYR* 3.4 49.4 - - + +
254A VAL* 3.7 14.1 - - + -
255A ARG* 3.8 10.0 - - + +
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Residues in contact with ALA 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A LEU* 3.9 11.7 - - + -
123A LYS 3.0 17.4 + - - +
124A ALA* 3.6 9.6 - - - +
125A LEU 3.3 0.2 - - - -
126A ALA* 1.3 74.7 - - - +
128A MSE 1.3 58.4 + - - +
130A LEU* 3.4 5.9 + - - +
131A ALA* 2.9 31.2 + - - +
254A VAL* 3.8 13.2 - - + +
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Residues in contact with MSE 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A LEU* 5.9 0.4 - - - -
72A LEU* 3.8 7.9 - - + +
77A LEU* 3.6 31.3 - - + +
124A ALA 2.9 18.3 + - - +
125A LEU* 3.4 27.4 - - + +
127A ALA* 1.3 74.5 - - - +
129A HIS* 1.3 73.7 + - + +
131A ALA* 3.3 1.9 + - - -
132A SER* 3.0 28.0 + - - -
189A VAL* 4.0 13.9 - - - +
190A ILE 4.4 1.1 - - - -
191A HIS* 3.2 42.6 - - + +
194A LEU* 5.5 0.2 - - + -
209A LEU* 4.0 10.8 - - + -
212A PHE* 4.2 15.9 - - + -
223A ASP* 3.6 2.7 - - - +
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Residues in contact with HIS 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A LEU* 2.9 32.3 + - + +
126A ALA 3.1 6.7 + - - +
128A MSE 1.3 80.0 - - - +
130A LEU* 1.3 62.4 + - - +
132A SER* 2.9 23.3 + - - -
133A GLU* 3.9 3.6 + - - +
188A GLY* 5.9 0.7 - - - -
189A VAL 3.6 19.1 - - - -
190A ILE* 4.1 1.2 - - - +
220A LEU* 3.5 51.3 - - + +
223A ASP* 2.8 28.0 + - + +
251A TYR* 2.7 34.4 + + - +
255A ARG* 4.6 3.6 - - - -
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Residues in contact with LEU 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A LYS* 5.0 2.6 - - - -
126A ALA 2.9 15.0 + - - +
127A ALA* 3.7 5.2 - - - +
129A HIS* 1.3 73.3 - - - +
131A ALA* 1.3 65.0 + - - +
132A SER 3.3 0.7 + - - -
133A GLU* 3.4 20.4 + - - +
254A VAL* 3.8 39.7 - - + +
255A ARG* 4.2 23.3 - - + +
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Residues in contact with ALA 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A HIS* 3.1 9.4 + - - -
72A LEU* 3.8 17.7 - - + +
75A LYS* 3.0 49.6 - - + +
77A LEU* 4.4 11.9 - - + +
127A ALA 2.9 20.1 + - - +
128A MSE 3.3 2.0 + - - +
130A LEU* 1.3 76.6 - - - +
132A SER* 1.3 58.4 + - - +
133A GLU 3.1 1.8 + - - -
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Residues in contact with SER 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A LEU* 4.5 5.2 - - - -
71A HIS* 4.0 4.0 - - - -
72A LEU* 3.8 13.2 - - - -
128A MSE 3.0 16.5 + - - -
129A HIS 2.9 16.3 + - - -
130A LEU 3.2 0.2 - - - -
131A ALA* 1.3 74.1 - - - +
133A GLU* 1.3 64.7 + - - +
134A GLY 3.4 0.2 + - - -
135A PHE* 3.3 21.5 + - - +
188A GLY* 4.9 1.0 - - - -
189A VAL* 3.5 48.7 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il